Not sure where else to turn for help with these subjects.
These subjects all came from the same scanner using the same protocol. Not sure what the difference could be. They’ve all been processed by fmriprep in the past (~1yr ago), but now that I’m processing again (starting with raw data -> BIDS using dcm2niix), I get errors like the following. Thanks for any help.
[Node] Finished "fmriprep_wf.single_subject_06_wf.func_preproc_run1_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
sys.exit(main())
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 465, in main
packagename='fmriprep')
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 478, in generate_reports
for subject_label in subject_list
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 478, in <listcomp>
for subject_label in subject_list
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 465, in run_reports
subject_id=subject_label, packagename=packagename)
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 267, in __init__
self._load_config(Path(config))
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 286, in _load_config
self.index(settings['sections'])
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 307, in index
for cfg in subrep_cfg['reportlets']]
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 307, in <listcomp>
for cfg in subrep_cfg['reportlets']]
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 164, in __init__
linked_svg = layout.build_path(entities, validate=False)
File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 1351, in build_path
raise ValueError("Unable to construct build path with source {}".format(source))
ValueError: Unable to construct build path with source {'datatype': 'figures', 'desc': 'bbregister', 'subject': '06', 'suffix': 'bold', 'extension': 'svg'}
fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues
fmriprep-docker --skip_bids_validation /Volumes/Data/Drive/Research/aim1 0 1.58s user 1.08s system 0% cpu 7:03:57.21 total
And here’s the log output:
Node: fmriprep_wf.single_subject_06_wf.summary
Working directory: /tmp/work/fmriprep_wf/single_subject_06_wf/summary
Node inputs:
bold = ['/data/sub-06/func/sub-06_run1_bold.nii.gz', '/data/sub-06/func/sub-06_run2_bold.nii.gz', '/data/sub-06/func/sub-06_run3_bold.nii.gz', '/data/sub-06/func/sub-06_run4_bold.nii.gz']
nstd_spaces = []
std_spaces = ['MNI152NLin2009cAsym', 'fsaverage5']
subject_id = 06
subjects_dir = /out/freesurfer
t1w = ['/data/sub-06/anat/sub-06_T1w.nii.gz']
t2w = <undefined>
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 336, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 395, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 100, in _run_interface
return super(SubjectSummary, self)._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 64, in _run_interface
segment = self._generate_segment()
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 124, in _generate_segment
for series in bold_series)
File "/usr/local/miniconda/lib/python3.7/collections/__init__.py", line 566, in __init__
self.update(*args, **kwds)
File "/usr/local/miniconda/lib/python3.7/collections/__init__.py", line 653, in update
_count_elements(self, iterable)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 124, in <genexpr>
for series in bold_series)
TypeError: 'NoneType' object is not subscriptable